It is now apparent that DNA can assume a variety of conformations that differ by degree from canonical B-form DNA. While the predominant form of DNA in vivo is almost certainly B-DNA, it is likely that alternative DNA structures play an important role in site-specific recognition of the DNA by proteins and other ligands and therefore in control of gene expression. Relatively little is known, however, about why certain DNA conformations are favored under some conditions but not others. Moreover, our understanding of the way in which structural variations in DNA serve as recognition signals for specific binding of proteins and other ligands is limited. In the experiments outlined in this proposal, high resolution nuclear magnetic resonance (NMR) spectroscopy (1- and 2-dimensional experiments, primarily 500MHz 1H) will be used to study the structure and dynamics of DNA oligomers which may adopt alternative (non-classical B-DNA) conformations in solution. Synthetic DNA oligomers will be studied in solution under a variety of conditions and in complex with drugs and proteins. Specific topics which will be addressed are: 1. Non-canonical Z-DNA (i.e. non-alternating C-G) structures and the conformation of the B-Z junction. 2. Hoogsteen base pairing in DNA induced by antibiotic (echinomycin) binding or other constraints on the DNA. 3. Conformations of DNA containing the naturally occuring modified bases m5C and m6A. Methylation of DNA is associated with restriction-modification systems in procaryotes, mis-match repair systems, and probably with control of gene regulation in eucaryotes. 4. Conformations of homopurine:homopyrimidine sequences of DNA. 5. Factors governing the conformational equilibria between these various DNA structures, e.g. the equilibria between B-DNA, Z-DNA, hairpin, bulge, and single-stranded DNA. These studies should help lead to an understanding of the role of alternative DNA conformations in protein and drug recognition and in genetic regulations.